{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);\n", "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb) >
"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Protein Design 2\n",
"\n",
"Keywords: FastDesign, FastRelax, ResidueSelector, TaskFactory, TaskOperation, pose_from_rcsb, get_residues_from_subset, ResidueNameSelector, ChainSelector, ResiduePropertySelector, NotResidueSelector, AndResidueSelector, RestrictToRepackingRLT, RestrictAbsentCanonicalAASRLT, NoRepackDisulfides, OperateOnResidueSubset\n",
"\n",
"## Overview\n",
"\n",
"Here, we will expand upon our knowledge of ResidueSelectors and TaskOperations and how to use them. We can once again use FastRelax or FastDesign to do design. Since we don't need any additional tools offered by FastDesign, we will use FastRelax. I like to call it RelaxedDesign. :)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"*Warning*: This notebook uses `pyrosetta.distributed.viewer` code, which runs in `jupyter notebook` and might not run if you're using `jupyterlab`."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"!pip install pyrosettacolabsetup\n",
"import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n",
"import pyrosetta; pyrosetta.init()\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Make sure you are in the directory with the pdb files:**\n",
"\n",
"`cd google_drive/MyDrive/student-notebooks/`"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
""
],
"text/plain": [
" "
]
}
],
"metadata": {
"celltoolbar": "Create Assignment",
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.1"
},
"toc": {
"base_numbering": 1,
"nav_menu": {},
"number_sections": true,
"sideBar": true,
"skip_h1_title": false,
"title_cell": "Table of Contents",
"title_sidebar": "Contents",
"toc_cell": false,
"toc_position": {},
"toc_section_display": true,
"toc_window_display": false
}
},
"nbformat": 4,
"nbformat_minor": 2
}